?As discussed yesterday with Jim, I've hit this problem:
- currently, sequences in the Desktop version hold dataset sequences, but the
applet sequences don't
- in the Desktop, SequenceFeatures are attached to the dataset sequence, in the
applet to the sequence
- there are about 65 calls to Sequence.getSequenceFeatures() with various
flavours of how to retrieve this data
- for cDNA/protein mapping to work in the applet, I want to create dataset
sequences - breaking some of this code
Suggested solution:
1) change method Sequence.getSequenceFeatures() so it searches the sequence or
dataset sequence until it finds sequence features (or not)
- i.e. use the same logic as currently in
FeatureRendererModel.findFeaturesAtRes()
2) track down and change any code that does this (example:
AlignmentSorter.sortByFeature())
SequenceFeatures sf = seq.getSequenceFeatures();
// remove these lines:
if (sf.getDatasetSequence() != null) {
sf = sf.getDatasetSequence().getSequenceFeatures();
}
I think that's the safest way to keep everything happy, but I'm open to
objections or better suggestions.
What I haven't explored is whether there are similar problems elsewhere
triggered by creating dataset sequences in the applet. Sequence.getDBRef()
might be a similar case?
Mungo
Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
College of Life Sciences
University of Dundee, Dundee, Scotland, UK.
www.jalview.org<http://www.jalview.org/>
www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk/>
The University of Dundee is a registered Scottish Charity, No: SC015096
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